Journal article

A community effort to create standards for evaluating tumor subclonal reconstruction

Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, Amit G Deshwar, Matei David, Nathan M Wilson, Stefan Dentro, Jeff A Wintersinger, Lydia Y Liu, Minjeong Ko, Srinivasan Sivanandan, Hongjiu Zhang, Kaiyi Zhu, Tai-Hsien Ou Yang, John M Chilton, Alex Buchanan, Christopher M Lalansingh, Christine P'ng, Catalina V Anghel, Imaad Umar Show all

Nature Biotechnology | NATURE RESEARCH | Published : 2020

Abstract

Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor a..

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